[3] Melkonian holds 16 patents[4] and is a co-founder of Algenion GmbH & Co. KG, an algal biotech company.
Melkonian studied the structure, function and development of the flagellar apparatus in algae[7] and co-discovered several centrosomal proteins novel for eukaryotes (e.g. centrin,[8] SF-assemblin).
[9] Through the study of the biogenesis of extracellular scales in green algae led to the revival of the cisternal maturation model of intra-Golgi apparatus.
[15] Molecular phylogenetic analyses helped to identify the flagellate Mesostigma as the earliest divergence in the Streptophyta[16] and the Zygnematophyceae as the likely sister group to the embryophyte land plants.
[17] Melkonian also worked on early research understanding the cercozoan photosynthetic amoeba Paulinella chromatophora, which has an independently evolved chloroplast called a chromatophore, and is an important example for the evolution of endosymbiotic organelles.